This PyMOL screenshot shows the alignment of two PDB structures, the first, a caspase-3 complexed with a nonpeptidic inhibitor (molecule shown as sticks) and the second, caspase-3 in complex with XIAP-BIR2 (shown as cartoon).

The image shows two crystal structures of human CDK2 in complex with inhibitors (1Y8Y, 2C6L). Structural interaction fingerprints (SIFts) were clustered (based on UniProt accession of the protein) and these two ligands were found to be neighbouring leaves on the same node. The structures can be loaded into PyMOL, aligned and the interactions visualised with command below. The resulting PyMOL scene can be downloaded from the bottom of this page.